IRESite_Id:404 characteristics of c-myc IRES studied in pML plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `404`	Version: `1`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-06-20 12:58:28`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
end-to-end_full-length_mRNA

The mRNA/+RNA description:

In vitro T3 run-off transcript containing 5' UTR of human c-myc (nt from -407 to -2) mRNA transcribed from
major P2 promoter cloned upstream of the luciferase reporter RNA lacking a poly (A) tail.

The mRNA/+RNA sequence represented in the +DNA notation:

GGGAACAAAA GCTGGGTACC GGGCCCCCCC TCGAGGTCGA CGGTATCGAT AAGCTTGATA TCGAATTCCT GCAGCCCGGG GGATCCACTA GAACTCGCTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TAGTAATTCC AGCGAGAGGC AGAGGGAGCG AGCGGGCGGC CGGCTAGGGT GGAAGAGCCG GGCGAGCAGA GCTGCGCTGC GGGCGTCCTG GGAAGGGAGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCCGGAGCGA ATAGGGGGCT TCGCCTCTGG CCCAGCCCTC CCGCTGATCC CCCAGCCAGC GGTCCGCAAC CCTTGCCGCA TCCACGAAAC TTTGCCCATA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCAGCGGGCG GGCACTTTGC ACTGGAACTT ACAACACCCG AGCAAGGACG CGACTCTCCC GACGCGGGGA GGCTATTCTG CCCATTTGGG GACACTTCCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGCCGCTGCC AGGACCCGCT TCTCTGAAAG GCTCTCCTTG CAGCTGCTTA GACGCTGGAT TTTTTTCGGG TAGTGGAAAA CCAGCAGCCT CCCGCGACCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGGCCGAAGA CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC ATTCTATCCT CTAGAGGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGCCCTGGTT CCTGGAACAA TTGCTTTTAC AGATGCACAT ATCGAGGTGA ACATCACGTA CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATGAAACGAT ATGGGCTGAA TACAAATCAC AGAATCGTCG TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTGCAGTTGC GCCCGCGAAC GACATTTATA ATGAACGTGA ATTGCTCAAC AGTATGAACA TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCAAAAAATT TTGAACGTGC AAAAAAAATT ACCAATAATC CAGAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTCGTCACAT CTCATCTACC TCCCGGTTTT AATGAATACG ATTTTGTACC AGAGTCCTTT GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GATCTACTGG GTTACCTAAG GGTGTGGCCC TTCCGCATAG AACTGCCTGC GTCAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GGATACTGCG ATTTTAAGTG TTGTTCCATT CCATCACGGT TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGATTTGAAG AAGAGCTGTT TTTACGATCC CTTCAGGATT ACAAAATTCA AAGTGCGTTG CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGATTGACAA ATACGATTTA TCTAATTTAC ACGAAATTGC TTCTGGGGGC GCACCTCTTT CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCCAGGGATA CGACAAGGAT ATGGGCTCAC TGAGACTACA TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CCATTTTTTG AAGCGAAGGT TGTGGATCTG GATACCGGGA AAACGCTGGG CGTTAATCAG AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTTATGTAAA CAATCCGGAA GCGACCAACG CCTTGATTGA CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CATAGTTGAC CGCTTGAAGT CTTTAATTAA ATACAAAGGA TATCAGGTGG CCCCCGCTGA ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCGGGCGTGG CAGGTCTTCC CGACGATGAC GCCGGTGAAC TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATTACGTCGC CAGTCAAGTA ACAACCGCGA AAAAGTTGCG CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAAAATCAGA GAGATCCTCA TAAAGGCCAA GAAGGGCGGA AAGTCCAAAT TGTAAGGATC CTCGAGTCTG AG
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pML The name of the promoter used to express this mRNA:
T3

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing 5' UTR of human c-myc transcribed from major P2 promoter (nt from -407 to -2) and firefly luciferase coding region (luc version of the luciferase gene) without the poly(A)tract.

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
c-myc

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HeLa S3 (ATCC CCL-2.2)

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

GTGGCACTTT TCGGGGAAAT GTGCGCGGAA CCCCTATTTG TTTATTTTTC TAAATACATT CAAATATGTA TCCGCTCATG AGACAATAAC CCTGATAAAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCTTCAATAA TATTGAAAAA GGAAGAGTAT GAGTATTCAA CATTTCCGTG TCGCCCTTAT TCCCTTTTTT GCGGCATTTT GCCTTCCTGT TTTTGCTCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCAGAAACGC TGGTGAAAGT AAAAGATGCT GAAGATCAGT TGGGTGCACG AGTGGGTTAC ATCGAACTGG ATCTCAACAG CGGTAAGATC CTTGAGAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCGCCCCGA AGAACGTTTT CCAATGATGA GCACTTTTAA AGTTCTGCTA TGTGGCGCGG TATTATCCCG TATTGACGCC GGGCAAGAGC AACTCGGTCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCGCATACAC TATTCTCAGA ATGACTTGGT TGAGTACTCA CCAGTCACAG AAAAGCATCT TACGGATGGC ATGACAGTAA GAGAATTATG CAGTGCTGCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATAACCATGA GTGATAACAC TGCGGCCAAC TTACTTCTGA CAACGATCGG AGGACCGAAG GAGCTAACCG CTTTTTTGCA CAACATGGGG GATCATGTAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CTCGCCTTGA TCGTTGGGAA CCGGAGCTGA ATGAAGCCAT ACCAAACGAC GAGCGTGACA CCACGATGCC TGTAGCAATG GCAACAACGT TGCGCAAACT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATTAACTGGC GAACTACTTA CTCTAGCTTC CCGGCAACAA TTAATAGACT GGATGGAGGC GGATAAAGTT GCAGGACCAC TTCTGCGCTC GGCCCTTCCG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCTGGCTGGT TTATTGCTGA TAAATCTGGA GCCGGTGAGC GTGGGTCTCG CGGTATCATT GCAGCACTGG GGCCAGATGG TAAGCCCTCC CGTATCGTAG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTATCTACAC GACGGGGAGT CAGGCAACTA TGGATGAACG AAATAGACAG ATCGCTGAGA TAGGTGCCTC ACTGATTAAG CATTGGTAAC TGTCAGACCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGTTTACTCA TATATACTTT AGATTGATTT AAAACTTCAT TTTTAATTTA AAAGGATCTA GGTGAAGATC CTTTTTGATA ATCTCATGAC CAAAATCCCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TAACGTGAGT TTTCGTTCCA CTGAGCGTCA GACCCCGTAG AAAAGATCAA AGGATCTTCT TGAGATCCTT TTTTTCTGCG CGTAATCTGC TGCTTGCAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAAAAAAACC ACCGCTACCA GCGGTGGTTT GTTTGCCGGA TCAAGAGCTA CCAACTCTTT TTCCGAAGGT AACTGGCTTC AGCAGAGCGC AGATACCAAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TACTGTCCTT CTAGTGTAGC CGTAGTTAGG CCACCACTTC AAGAACTCTG TAGCACCGCC TACATACCTC GCTCTGCTAA TCCTGTTACC AGTGGCTGCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCCAGTGGCG ATAAGTCGTG TCTTACCGGG TTGGACTCAA GACGATAGTT ACCGGATAAG GCGCAGCGGT CGGGCTGAAC GGGGGGTTCG TGCACACAGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCAGCTTGGA GCGAACGACC TACACCGAAC TGAGATACCT ACAGCGTGAG CTATGAGAAA GCGCCACGCT TCCCGAAGGG AGAAAGGCGG ACAGGTATCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGTAAGCGGC AGGGTCGGAA CAGGAGAGCG CACGAGGGAG CTTCCAGGGG GAAACGCCTG GTATCTTTAT AGTCCTGTCG GGTTTCGCCA CCTCTGACTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGCGTCGAT TTTTGTGATG CTCGTCAGGG GGGCGGAGCC TATGGAAAAA CGCCAGCAAC GCGGCCTTTT TACGGTTCCT GGCCTTTTGC TGGCCTTTTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCACATGTT CTTTCCTGCG TTATCCCCTG ATTCTGTGGA TAACCGTATT ACCGCCTTTG AGTGAGCTGA TACCGCTCGC CGCAGCCGAA CGACCGAGCG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CAGCGAGTCA GTGAGCGAGG AAGCGGAAGA GCGCCCAATA CGCAAACCGC CTCTCCCCGC GCGTTGGCCG ATTCATTAAT GCAGCTGGCA CGACAGGTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCCGACTGGA AAGCGGGCAG TGAGCGCAAC GCAATTAATG TGAGTTAGCT CACTCATTAG GCACCCCAGG CTTTACACTT TATGCTTCCG GCTCGTATGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGTGTGGAAT TGTGAGCGGA TAACAATTTC ACACAGGAAA CAGCTATGAC CATGATTACG CCAAGCGCGC AATTAACCCT CACTAAAGGG AACAAAAGCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGGTACCGGG CCCCCCCTCG AGGTCGACGG TATCGATAAG CTTGATATCG AATTCCTGCA GCCCGGGGGA TCCACTAGAA CTCGCTGTAG TAATTCCAGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAGAGGCAGA GGGAGCGAGC GGGCGGCCGG CTAGGGTGGA AGAGCCGGGC GAGCAGAGCT GCGCTGCGGG CGTCCTGGGA AGGGAGATCC GGAGCGAATA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GGGGGCTTCG CCTCTGGCCC AGCCCTCCCG CTGATCCCCC AGCCAGCGGT CCGCAACCCT TGCCGCATCC ACGAAACTTT GCCCATAGCA GCGGGCGGGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACTTTGCACT GGAACTTACA ACACCCGAGC AAGGACGCGA CTCTCCCGAC GCGGGGAGGC TATTCTGCCC ATTTGGGGAC ACTTCCCCGC CGCTGCCAGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACCCGCTTCT CTGAAAGGCT CTCCTTGCAG CTGCTTAGAC GCTGGATTTT TTTCGGGTAG TGGAAAACCA GCAGCCTCCC GCGACCATGG CCGAAGACGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAAAAACATA AAGAAAGGCC CGGCGCCATT CTATCCTCTA GAGGATGGAA CCGCTGGAGA GCAACTGCAT AAGGCTATGA AGAGATACGC CCTGGTTCCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGAACAATTG CTTTTACAGA TGCACATATC GAGGTGAACA TCACGTACGC GGAATACTTC GAAATGTCCG TTCGGTTGGC AGAAGCTATG AAACGATATG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCTGAATAC AAATCACAGA ATCGTCGTAT GCAGTGAAAA CTCTCTTCAA TTCTTTATGC CGGTGTTGGG CGCGTTATTT ATCGGAGTTG CAGTTGCGCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGCGAACGAC ATTTATAATG AACGTGAATT GCTCAACAGT ATGAACATTT CGCAGCCTAC CGTAGTGTTT GTTTCCAAAA AGGGGTTGCA AAAAATTTTG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AACGTGCAAA AAAAATTACC AATAATCCAG AAAATTATTA TCATGGATTC TAAAACGGAT TACCAGGGAT TTCAGTCGAT GTACACGTTC GTCACATCTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ATCTACCTCC CGGTTTTAAT GAATACGATT TTGTACCAGA GTCCTTTGAT CGTGACAAAA CAATTGCACT GATAATGAAT TCCTCTGGAT CTACTGGGTT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACCTAAGGGT GTGGCCCTTC CGCATAGAAC TGCCTGCGTC AGATTCTCGC ATGCCAGAGA TCCTATTTTT GGCAATCAAA TCATTCCGGA TACTGCGATT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTAAGTGTTG TTCCATTCCA TCACGGTTTT GGAATGTTTA CTACACTCGG ATATTTGATA TGTGGATTTC GAGTCGTCTT AATGTATAGA TTTGAAGAAG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCTGTTTTT ACGATCCCTT CAGGATTACA AAATTCAAAG TGCGTTGCTA GTACCAACCC TATTTTCATT CTTCGCCAAA AGCACTCTGA TTGACAAATA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGATTTATCT AATTTACACG AAATTGCTTC TGGGGGCGCA CCTCTTTCGA AAGAAGTCGG GGAAGCGGTT GCAAAACGCT TCCATCTTCC AGGGATACGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CAAGGATATG GGCTCACTGA GACTACATCA GCTATTCTGA TTACACCCGA GGGGGATGAT AAACCGGGCG CGGTCGGTAA AGTTGTTCCA TTTTTTGAAG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CGAAGGTTGT GGATCTGGAT ACCGGGAAAA CGCTGGGCGT TAATCAGAGA GGCGAATTAT GTGTCAGAGG ACCTATGATT ATGTCCGGTT ATGTAAACAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TCCGGAAGCG ACCAACGCCT TGATTGACAA GGATGGATGG CTACATTCTG GAGACATAGC TTACTGGGAC GAAGACGAAC ACTTCTTCAT AGTTGACCGC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TTGAAGTCTT TAATTAAATA CAAAGGATAT CAGGTGGCCC CCGCTGAATT GGAATCGATA TTGTTACAAC ACCCCAACAT CTTCGACGCG GGCGTGGCAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTCTTCCCGA CGATGACGCC GGTGAACTTC CCGCCGCCGT TGTTGTTTTG GAGCACGGAA AGACGATGAC GGAAAAAGAG ATCGTGGATT ACGTCGCCAG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TCAAGTAACA ACCGCGAAAA AGTTGCGCGG AGGAGTTGTG TTTGTGGACG AAGTACCGAA AGGTCTTACC GGAAAACTCG ACGCAAGAAA AATCAGAGAG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ATCCTCATAA AGGCCAAGAA GGGCGGAAAG TCCAAATTGT AAGGATCCTC GAGTCTGAGC TCCAATTCGC CCTATAGTGA GTCGTATTAC GCGCGCTCAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TGGCCGTCGT TTTACAACGT CGTGACTGGG AAAACCCTGG CGTTACCCAA CTTAATCGCC TTGCAGCACA TCCCCCTTTC GCCAGCTGGC GTAATAGCGA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AGAGGCCCGC ACCGATCGCC CTTCCCAACA GTTGCGCAGC CTGAATGGCG AATGGGACGC GCCCTGTAGC GGCGCATTAA GCGCGGCGGG TGTGGTGGTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACGCGCAGCG TGACCGCTAC ACTTGCCAGC GCCCTAGCGC CCGCTCCTTT CGCTTTCTTC CCTTCCTTTC TCGCCACGTT CGCCGGCTTT CCCCGTCAAG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTCTAAATCG GGGGCTCCCT TTAGGGTTCC GATTTAGTGC TTTACGGCAC CTCGACCCCA AAAAACTTGA TTAGGGTGAT GGTTCACGTA GTGGGCCATC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GCCCTGATAG ACGGTTTTTC GCCCTTTGAC GTTGGAGTCC ACGTTCTTTA ATAGTGGACT CTTGTTCCAA ACTGGAACAA CACTCAACCC TATCTCGGTC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TATTCTTTTG ATTTATAAGG GATTTTGCCG ATTTCGGCCT ATTGGTTAAA AAATGAGCTG ATTTAACAAA AATTTAACGC GAATTTTAAC AAAATATTAA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CGCTTACAAT TTAG
^5001      ^5011

Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):

plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

1

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FFluc

The description of the protein encoded in this ORF:
firefly luciferase

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

The ORF absolute position (the base range includes START and STOP codons or their equivalents):

500-2155

Remarks:

IRESite notes about verification of plasmid sequence:
The complete sequence of IRES element was determined by sequencing using Fluc_seq_reverse
(AGGAACCAGGGCGTATCTC) primer.

For detailed verification of whole plasmid sequence see item IRESite Id: 413.

Citations:

Thoma C., Bergamini G., Galy B., Hundsdoerfer P., Hentze M. W. (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol. Cell. 15(6):925-935

IRESs:

IRES:

Version: `1`	Last change: `2008-06-19 14:18:19`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `c-myc`	The functional status of IRES: `functional`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

92-498

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

AACTCGCTGT AGTAATTCCA GCGAGAGGCA GAGGGAGCGA GCGGGCGGCC GGCTAGGGTG GAAGAGCCGG GCGAGCAGAG CTGCGCTGCG GGCGTCCTGG 
^92        ^102       ^112       ^122       ^132       ^142       ^152       ^162       ^172       ^182       

GAAGGGAGAT CCGGAGCGAA TAGGGGGCTT CGCCTCTGGC CCAGCCCTCC CGCTGATCCC CCAGCCAGCG GTCCGCAACC CTTGCCGCAT CCACGAAACT 
^192       ^202       ^212       ^222       ^232       ^242       ^252       ^262       ^272       ^282       

TTGCCCATAG CAGCGGGCGG GCACTTTGCA CTGGAACTTA CAACACCCGA GCAAGGACGC GACTCTCCCG ACGCGGGGAG GCTATTCTGC CCATTTGGGG 
^292       ^302       ^312       ^322       ^332       ^342       ^352       ^362       ^372       ^382       

ACACTTCCCC GCCGCTGCCA GGACCCGCTT CTCTGAAAGG CTCTCCTTGC AGCTGCTTAG ACGCTGGATT TTTTTCGGGT AGTGGAAAAC CAGCAGCCTC 
^392       ^402       ^412       ^422       ^432       ^442       ^452       ^462       ^472       ^482       

CCGCGAC
^492

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 461

Version: `3`	Last change: `2008-06-20 12:58:28`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vitro The in vitro translation system:
HeLa cell lysate

The organism used for translation:

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

31.500

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pML-p(A)`	Name of the plasmid used as the negative control. `pMiL`
`IRESite Id` of the plasmid used as positive control. `403`	`IRESite Id` of the plasmid used as negative control. `399`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `7.800`

The effect of 5'-cap analogs on translation:
no

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_ApppG_cap_without_polyA_tail

Remarks:

The translation of c-myc.IRES RNA is about 3-fold less efficient than the translation of the polyadenylated
counterpart c-myc.IRES-pA RNA (IRESite ID: 399).

Translational data are derived from Fig. 1A.

Citations:

Translation results:

IRESite Translation Id: 462

Version: `1`	Last change: `2008-06-19 10:54:01`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

0

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pMiL-p(A)`	Name of the plasmid used as the negative control. `pNO-IRES`
`IRESite Id` of the plasmid used as positive control. `403`	`IRESite Id` of the plasmid used as negative control. `394`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_ApppG_cap_without_polyA_tail

Remarks:

The poly(A) tail is essential for cellular IRES-driven translation in transfected cells.
RNAs lacking a poly(A) tail are poorly translated, only the presence of a poly(A) tail essentially enables
translation (see IRESId: 403)

Translational data are derived from Fig. 2A.

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1